support multimer (#54)

README.md

@@ -59,7 +59,7 @@ Run the following command to build a docker image from Dockerfile provided.
 
 ```shell
 cd ColossalAI
-docker build -t fastfold ./docker
+docker build -t Fastfold ./docker
 ```
 
 Run the following command to start the docker container in interactive mode.

fastfold/config.py

@@ -74,6 +74,24 @@ def model_config(name, train=False, low_prec=False):
         c.model.template.enabled = False
         c.model.heads.tm.enabled = True
         c.loss.tm.weight = 0.1
+    elif name == "relax":
+        pass
+    elif "multimer" in name:
+        c.globals.is_multimer = True
+        c.data.predict.max_msa_clusters = 252  # 128 for monomer
+        c.model.structure_module.trans_scale_factor = 20  # 10 for monomer
+        for k, v in multimer_model_config_update.items():
+            c.model[k] = v
+
+        c.data.common.unsupervised_features.extend(
+            [
+                "msa_mask",
+                "seq_mask",
+                "asym_id",
+                "entity_id",
+                "sym_id",
+            ]
+        )
     else:
         raise ValueError("Invalid model name")
 
@@ -275,6 +293,7 @@ config = mlc.ConfigDict(
             "c_e": c_e,
             "c_s": c_s,
             "eps": eps,
+            "is_multimer": False,
         },
         "model": {
             "_mask_trans": False,
@@ -494,4 +513,77 @@ config = mlc.ConfigDict(
         },
         "ema": {"decay": 0.999},
     }
-)
\ No newline at end of file
+)
+
+multimer_model_config_update = {
+    "input_embedder": {
+        "tf_dim": 21,
+        "msa_dim": 49,
+        "c_z": c_z,
+        "c_m": c_m,
+        "relpos_k": 32,
+        "max_relative_chain": 2,
+        "max_relative_idx": 32,
+        "use_chain_relative": True,
+    },
+    "template": {
+        "distogram": {
+            "min_bin": 3.25,
+            "max_bin": 50.75,
+            "no_bins": 39,
+        },
+        "template_pair_embedder": {
+            "c_z": c_z,
+            "c_out": 64,
+            "c_dgram": 39,
+            "c_aatype": 22,
+        },
+        "template_single_embedder": {
+            "c_in": 34,
+            "c_m": c_m,
+        },
+        "template_pair_stack": {
+            "c_t": c_t,
+            # DISCREPANCY: c_hidden_tri_att here is given in the supplement
+            # as 64. In the code, it's 16.
+            "c_hidden_tri_att": 16,
+            "c_hidden_tri_mul": 64,
+            "no_blocks": 2,
+            "no_heads": 4,
+            "pair_transition_n": 2,
+            "dropout_rate": 0.25,
+            "blocks_per_ckpt": blocks_per_ckpt,
+            "inf": 1e9,
+        },
+        "c_t": c_t,
+        "c_z": c_z,
+        "inf": 1e5,  # 1e9,
+        "eps": eps,  # 1e-6,
+        "enabled": templates_enabled,
+        "embed_angles": embed_template_torsion_angles,
+    },
+    "heads": {
+        "lddt": {
+            "no_bins": 50,
+            "c_in": c_s,
+            "c_hidden": 128,
+        },
+        "distogram": {
+            "c_z": c_z,
+            "no_bins": aux_distogram_bins,
+        },
+        "tm": {
+            "c_z": c_z,
+            "no_bins": aux_distogram_bins,
+            "enabled": tm_enabled,
+        },
+        "masked_msa": {
+            "c_m": c_m,
+            "c_out": 22,
+        },
+        "experimentally_resolved": {
+            "c_s": c_s,
+            "c_out": 37,
+        },
+    },
+}

fastfold/data/tools/hmmsearch.py

+# Copyright 2021 DeepMind Technologies Limited
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#            http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""A Python wrapper for hmmsearch - search profile against a sequence db."""
+
+import os
+import subprocess
+import logging
+from typing import Optional, Sequence
+
+from fastfold.data import parsers
+from fastfold.data.tools import hmmbuild
+from fastfold.utils import general_utils as utils
+
+class Hmmsearch(object):
+    """Python wrapper of the hmmsearch binary."""
+
+    def __init__(
+        self,
+        *,
+        binary_path: str,
+        hmmbuild_binary_path: str,
+        database_path: str,
+        flags: Optional[Sequence[str]] = None,
+    ):
+        """Initializes the Python hmmsearch wrapper.
+
+        Args:
+            binary_path: The path to the hmmsearch executable.
+            hmmbuild_binary_path: The path to the hmmbuild executable. Used to build
+                an hmm from an input a3m.
+            database_path: The path to the hmmsearch database (FASTA format).
+            flags: List of flags to be used by hmmsearch.
+
+        Raises:
+            RuntimeError: If hmmsearch binary not found within the path.
+        """
+        self.binary_path = binary_path
+        self.hmmbuild_runner = hmmbuild.Hmmbuild(binary_path=hmmbuild_binary_path)
+        self.database_path = database_path
+        if flags is None:
+            # Default hmmsearch run settings.
+            flags = [
+                "--F1",
+                "0.1",
+                "--F2",
+                "0.1",
+                "--F3",
+                "0.1",
+                "--incE",
+                "100",
+                "-E",
+                "100",
+                "--domE",
+                "100",
+                "--incdomE",
+                "100",
+            ]
+        self.flags = flags
+
+        if not os.path.exists(self.database_path):
+            logging.error("Could not find hmmsearch database %s", database_path)
+            raise ValueError(f"Could not find hmmsearch database {database_path}")
+
+    @property
+    def output_format(self) -> str:
+        return "sto"
+
+    @property
+    def input_format(self) -> str:
+        return "sto"
+
+    def query(self, msa_sto: str, output_dir: Optional[str] = None) -> str:
+        """Queries the database using hmmsearch using a given stockholm msa."""
+        hmm = self.hmmbuild_runner.build_profile_from_sto(
+            msa_sto, model_construction="hand"
+        )
+        return self.query_with_hmm(hmm, output_dir)
+
+    def query_with_hmm(self, hmm: str, output_dir: Optional[str] = None) -> str:
+        """Queries the database using hmmsearch using a given hmm."""
+        with utils.tmpdir_manager() as query_tmp_dir:
+            hmm_input_path = os.path.join(query_tmp_dir, "query.hmm")
+            output_dir = query_tmp_dir if output_dir is None else output_dir
+            out_path = os.path.join(output_dir, "hmm_output.sto")
+            with open(hmm_input_path, "w") as f:
+                f.write(hmm)
+
+            cmd = [
+                self.binary_path,
+                "--noali",  # Don't include the alignment in stdout.
+                "--cpu",
+                "8",
+            ]
+            # If adding flags, we have to do so before the output and input:
+            if self.flags:
+                cmd.extend(self.flags)
+            cmd.extend(
+                [
+                    "-A",
+                    out_path,
+                    hmm_input_path,
+                    self.database_path,
+                ]
+            )
+
+            logging.info("Launching sub-process %s", cmd)
+            process = subprocess.Popen(
+                cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE
+            )
+            with utils.timing(
+                f"hmmsearch ({os.path.basename(self.database_path)}) query"
+            ):
+                stdout, stderr = process.communicate()
+                retcode = process.wait()
+
+            if retcode:
+                raise RuntimeError(
+                    "hmmsearch failed:\nstdout:\n%s\n\nstderr:\n%s\n"
+                    % (stdout.decode("utf-8"), stderr.decode("utf-8"))
+                )
+
+            with open(out_path) as f:
+                out_msa = f.read()
+
+        return out_msa
+
+    @staticmethod
+    def get_template_hits(
+        output_string: str, input_sequence: str
+    ) -> Sequence[parsers.TemplateHit]:
+        """Gets parsed template hits from the raw string output by the tool."""
+        template_hits = parsers.parse_hmmsearch_sto(
+            output_string,
+            input_sequence,
+        )
+        return template_hits

fastfold/distributed/comm.py

@@ -43,7 +43,7 @@ def _gather(tensor: Tensor, dim: int = -1) -> Tensor:
     if gpc.get_world_size(ParallelMode.TENSOR) == 1:
         return tensor
 
-    if dim == 1:
+    if dim == 1 and list(tensor.shape)[0] == 1:
         output_shape = list(tensor.shape)
         output_shape[1] *= gpc.get_world_size(ParallelMode.TENSOR)
         output = torch.empty(output_shape, dtype=tensor.dtype, device=tensor.device)

fastfold/model/fastnn/blocks.py

@@ -32,7 +32,7 @@ from fastfold.distributed.comm_async import All_to_All_Async, All_to_All_Async_O
 
 class EvoformerBlock(nn.Module):
 
-    def __init__(self, c_m: int, c_z: int, first_block: bool, last_block: bool):
+    def __init__(self, c_m: int, c_z: int, first_block: bool, last_block: bool, is_multimer: bool=False):
         super(EvoformerBlock, self).__init__()
 
         self.first_block = first_block
@@ -41,6 +41,7 @@ class EvoformerBlock(nn.Module):
         self.msa_stack = MSAStack(c_m, c_z, p_drop=0.15)
         self.communication = OutProductMean(n_feat=c_m, n_feat_out=c_z, n_feat_proj=32)
         self.pair_stack = PairStack(d_pair=c_z)
+        self.is_multimer = is_multimer 
 
     def forward(
         self,
@@ -73,12 +74,19 @@ class EvoformerBlock(nn.Module):
         msa_mask = torch.nn.functional.pad(msa_mask, (0, padding_size))
         pair_mask = torch.nn.functional.pad(pair_mask, (0, padding_size, 0, padding_size))
 
-        m = self.msa_stack(m, z, msa_mask)
-
-        z = z + self.communication(m, msa_mask)
-        m, work = All_to_All_Async.apply(m, 1, 2)
-        z = self.pair_stack(z, pair_mask)
-        m = All_to_All_Async_Opp.apply(m, work, 1, 2)
+        if not self.is_multimer:
+            m = self.msa_stack(m, z, msa_mask)
+            z = z + self.communication(m, msa_mask)
+            m, work = All_to_All_Async.apply(m, 1, 2)
+            z = self.pair_stack(z, pair_mask)
+            m = All_to_All_Async_Opp.apply(m, work, 1, 2)
+        else:
+            z = z + self.communication(m, msa_mask)
+            z_ori = z
+            m, work = All_to_All_Async.apply(m, 1, 2)
+            z = self.pair_stack(z, pair_mask)
+            m = All_to_All_Async_Opp.apply(m, work, 1, 2)
+            m = self.msa_stack(m, z_ori, msa_mask)
 
         if self.last_block:
             m = m.squeeze(0)
@@ -260,7 +268,6 @@ class TemplatePairStackBlock(nn.Module):
             single_templates[i] = single
 
         z = torch.cat(single_templates, dim=-4)
-
         if self.last_block:
             z = gather(z, dim=1)
             z = z[:, :-padding_size, :-padding_size, :]

fastfold/model/hub/alphafold.py

@@ -26,6 +26,7 @@ from fastfold.utils.feats import (
 )
 from fastfold.model.nn.embedders import (
     InputEmbedder,
+    InputEmbedderMultimer,
     RecyclingEmbedder,
     TemplateAngleEmbedder,
     TemplatePairEmbedder,
@@ -69,9 +70,14 @@ class AlphaFold(nn.Module):
         extra_msa_config = config.extra_msa
 
         # Main trunk + structure module
-        self.input_embedder = InputEmbedder(
-            **config["input_embedder"],
-        )
+        if self.globals.is_multimer:
+            self.input_embedder = InputEmbedderMultimer(
+                **config["input_embedder"],
+            )
+        else:   
+            self.input_embedder = InputEmbedder(
+                **config["input_embedder"],
+            )
         self.recycling_embedder = RecyclingEmbedder(
             **config["recycling_embedder"],
         )

fastfold/model/nn/embedders.py

@@ -15,7 +15,7 @@
 
 import torch
 import torch.nn as nn
-from typing import Tuple
+from typing import Tuple, Dict
 
 from fastfold.model.nn.primitives import Linear, LayerNorm
 from fastfold.utils.tensor_utils import one_hot
@@ -125,6 +125,146 @@ class InputEmbedder(nn.Module):
 
         return msa_emb, pair_emb
 
+class InputEmbedderMultimer(nn.Module):
+    """
+    Embeds a subset of the input features.
+
+    Implements Algorithms 3 (InputEmbedder) and 4 (relpos).
+    """
+
+    def __init__(
+        self,
+        tf_dim: int,
+        msa_dim: int,
+        c_z: int,
+        c_m: int,
+        max_relative_idx: int,
+        use_chain_relative: bool,
+        max_relative_chain: int,
+        **kwargs,
+    ):
+        """
+        Args:
+            tf_dim:
+                Final dimension of the target features
+            msa_dim:
+                Final dimension of the MSA features
+            c_z:
+                Pair embedding dimension
+            c_m:
+                MSA embedding dimension
+            relpos_k:
+                Window size used in relative positional encoding
+        """
+        super(InputEmbedderMultimer, self).__init__()
+
+        self.tf_dim = tf_dim
+        self.msa_dim = msa_dim
+
+        self.c_z = c_z
+        self.c_m = c_m
+
+        self.linear_tf_z_i = Linear(tf_dim, c_z)
+        self.linear_tf_z_j = Linear(tf_dim, c_z)
+        self.linear_tf_m = Linear(tf_dim, c_m)
+        self.linear_msa_m = Linear(msa_dim, c_m)
+
+        # RPE stuff
+        self.max_relative_idx = max_relative_idx
+        self.use_chain_relative = use_chain_relative
+        self.max_relative_chain = max_relative_chain
+        if self.use_chain_relative:
+            self.no_bins = 2 * max_relative_idx + 2 + 1 + 2 * max_relative_chain + 2
+        else:
+            self.no_bins = 2 * max_relative_idx + 1
+        self.linear_relpos = Linear(self.no_bins, c_z)
+
+    def relpos(self, batch: Dict[str, torch.Tensor]):
+        pos = batch["residue_index"]
+        asym_id = batch["asym_id"]
+        asym_id_same = asym_id[..., None] == asym_id[..., None, :]
+        offset = pos[..., None] - pos[..., None, :]
+
+        clipped_offset = torch.clamp(
+            offset + self.max_relative_idx, 0, 2 * self.max_relative_idx
+        )
+
+        rel_feats = []
+        if self.use_chain_relative:
+            final_offset = torch.where(
+                asym_id_same,
+                clipped_offset,
+                (2 * self.max_relative_idx + 1) * torch.ones_like(clipped_offset),
+            )
+
+            rel_pos = torch.nn.functional.one_hot(
+                final_offset,
+                2 * self.max_relative_idx + 2,
+            )
+
+            rel_feats.append(rel_pos)
+
+            entity_id = batch["entity_id"]
+            entity_id_same = entity_id[..., None] == entity_id[..., None, :]
+            rel_feats.append(entity_id_same[..., None])
+
+            sym_id = batch["sym_id"]
+            rel_sym_id = sym_id[..., None] - sym_id[..., None, :]
+
+            max_rel_chain = self.max_relative_chain
+            clipped_rel_chain = torch.clamp(
+                rel_sym_id + max_rel_chain,
+                0,
+                2 * max_rel_chain,
+            )
+
+            final_rel_chain = torch.where(
+                entity_id_same,
+                clipped_rel_chain,
+                (2 * max_rel_chain + 1) * torch.ones_like(clipped_rel_chain),
+            )
+
+            rel_chain = torch.nn.functional.one_hot(
+                final_rel_chain.long(),
+                2 * max_rel_chain + 2,
+            )
+
+            rel_feats.append(rel_chain)
+        else:
+            rel_pos = torch.nn.functional.one_hot(
+                clipped_offset,
+                2 * self.max_relative_idx + 1,
+            )
+            rel_feats.append(rel_pos)
+
+        rel_feat = torch.cat(rel_feats, dim=-1).to(self.linear_relpos.weight.dtype)
+
+        return self.linear_relpos(rel_feat)
+
+    def forward(
+        self, batch: Dict[str, torch.Tensor]
+    ) -> Tuple[torch.Tensor, torch.Tensor]:
+        tf = batch["target_feat"]
+        msa = batch["msa_feat"]
+
+        # [*, N_res, c_z]
+        tf_emb_i = self.linear_tf_z_i(tf)
+        tf_emb_j = self.linear_tf_z_j(tf)
+
+        # [*, N_res, N_res, c_z]
+        pair_emb = tf_emb_i[..., None, :] + tf_emb_j[..., None, :, :]
+        pair_emb = pair_emb + self.relpos(batch)
+
+        # [*, N_clust, N_res, c_m]
+        n_clust = msa.shape[-3]
+        tf_m = (
+            self.linear_tf_m(tf)
+            .unsqueeze(-3)
+            .expand(((-1,) * len(tf.shape[:-2]) + (n_clust, -1, -1)))
+        )
+        msa_emb = self.linear_msa_m(msa) + tf_m
+
+        return msa_emb, pair_emb
 
 class RecyclingEmbedder(nn.Module):
     """

fastfold/model/nn/template.py

@@ -142,6 +142,7 @@ class TemplatePairStackBlock(nn.Module):
         pair_transition_n: int,
         dropout_rate: float,
         inf: float,
+        is_multimer: bool=False,
         **kwargs,
     ):
         super(TemplatePairStackBlock, self).__init__()
@@ -153,6 +154,7 @@ class TemplatePairStackBlock(nn.Module):
         self.pair_transition_n = pair_transition_n
         self.dropout_rate = dropout_rate
         self.inf = inf
+        self.is_multimer = is_multimer
 
         self.dropout_row = DropoutRowwise(self.dropout_rate)
         self.dropout_col = DropoutColumnwise(self.dropout_rate)
@@ -196,43 +198,67 @@ class TemplatePairStackBlock(nn.Module):
         single_templates_masks = [
             m.unsqueeze(-3) for m in torch.unbind(mask, dim=-3)
         ]
-        for i in range(len(single_templates)):
-            single = single_templates[i]
-            single_mask = single_templates_masks[i]
-            
-            single = single + self.dropout_row(
-                self.tri_att_start(
-                    single,
-                    chunk_size=chunk_size,
-                    mask=single_mask
+        if not self.is_multimer:
+            for i in range(len(single_templates)):
+                single = single_templates[i]
+                single_mask = single_templates_masks[i]
+                
+                single = single + self.dropout_row(
+                    self.tri_att_start(
+                        single,
+                        chunk_size=chunk_size,
+                        mask=single_mask
+                    )
                 )
-            )
-            single = single + self.dropout_col(
-                self.tri_att_end(
+                single = single + self.dropout_col(
+                    self.tri_att_end(
+                        single,
+                        chunk_size=chunk_size,
+                        mask=single_mask
+                    )
+                )
+                single = single + self.dropout_row(
+                    self.tri_mul_out(
+                        single,
+                        mask=single_mask
+                    )
+                )
+                single = single + self.dropout_row(
+                    self.tri_mul_in(
+                        single,
+                        mask=single_mask
+                    )
+                )
+                single = single + self.pair_transition(
                     single,
+                    mask=single_mask if _mask_trans else None,
                     chunk_size=chunk_size,
-                    mask=single_mask
                 )
-            )
-            single = single + self.dropout_row(
-                self.tri_mul_out(
-                    single,
-                    mask=single_mask
+
+                single_templates[i] = single
+        else:
+            for i in range(len(single_templates)):
+                single = single_templates[i]
+                single_mask = single_templates_masks[i]
+
+                single = single + self.dropout_row(
+                    self.tri_att_start(single, chunk_size=chunk_size, mask=single_mask)
                 )
-            )
-            single = single + self.dropout_row(
-                self.tri_mul_in(
+                single = single + self.dropout_col(
+                    self.tri_att_end(single, chunk_size=chunk_size, mask=single_mask)
+                )
+                single = single + self.dropout_row(
+                    self.tri_mul_out(single, mask=single_mask)
+                )
+                single = single + self.dropout_row(
+                    self.tri_mul_in(single, mask=single_mask)
+                )
+                single = single + self.pair_transition(
                     single,
-                    mask=single_mask
+                    mask=single_mask if _mask_trans else None,
+                    chunk_size=chunk_size,
                 )
-            )
-            single = single + self.pair_transition(
-                single,
-                mask=single_mask if _mask_trans else None,
-                chunk_size=chunk_size,
-            )
-
-            single_templates[i] = single
+                single_templates[i] = single
 
         z = torch.cat(single_templates, dim=-4)
 

fastfold/workflow/template/fastfold_data_workflow.py

 import os
 import time
 from multiprocessing import cpu_count
+import ray
 from ray import workflow
 from fastfold.workflow.factory import JackHmmerFactory, HHSearchFactory, HHBlitsFactory
 from fastfold.workflow import batch_run
@@ -80,6 +81,7 @@ class FastFoldDataWorkFlow:
             print("Workflow not found. Clean. Skipping")
             pass
 
+        
         # prepare alignment directory for alignment outputs
         if alignment_dir is None:
             alignment_dir = os.path.join(output_dir, "alignment")

inference.py

@@ -23,6 +23,7 @@ from datetime import date
 import numpy as np
 import torch
 import torch.multiprocessing as mp
+import pickle
 from fastfold.model.hub import AlphaFold
 
 import fastfold
@@ -111,6 +112,7 @@ def inference_model(rank, world_size, result_q, batch, args):
 
 def main(args):
     config = model_config(args.model_name)
+    global_is_multimer = True if args.model_preset == "multimer" else False
 
     template_featurizer = templates.TemplateHitFeaturizer(
         mmcif_dir=args.template_mmcif_dir,
@@ -147,6 +149,7 @@ def main(args):
     seqs, tags = parse_fasta(fasta)
 
     for tag, seq in zip(tags, seqs):
+        print(f"tag:{tag} seq:{seq}")
         batch = [None]
         
         fasta_path = os.path.join(args.output_dir, "tmp.fasta")
@@ -155,44 +158,48 @@ def main(args):
 
         print("Generating features...")
         local_alignment_dir = os.path.join(alignment_dir, tag)
-        if (args.use_precomputed_alignments is None):
-            if not os.path.exists(local_alignment_dir):
-                os.makedirs(local_alignment_dir)
-            if args.enable_workflow:
-                print("Running alignment with ray workflow...")
-                alignment_data_workflow_runner = FastFoldDataWorkFlow(
-                    jackhmmer_binary_path=args.jackhmmer_binary_path,
-                    hhblits_binary_path=args.hhblits_binary_path,
-                    hhsearch_binary_path=args.hhsearch_binary_path,
-                    uniref90_database_path=args.uniref90_database_path,
-                    mgnify_database_path=args.mgnify_database_path,
-                    bfd_database_path=args.bfd_database_path,
-                    uniclust30_database_path=args.uniclust30_database_path,
-                    pdb70_database_path=args.pdb70_database_path,
-                    use_small_bfd=use_small_bfd,
-                    no_cpus=args.cpus,
-                    )
-                t = time.perf_counter()
-                alignment_data_workflow_runner.run(fasta_path, output_dir=output_dir_base, alignment_dir=local_alignment_dir)
-                print(f"Alignment data workflow time: {time.perf_counter() - t}")
-            else:
-                alignment_runner = data_pipeline.AlignmentRunner(
-                    jackhmmer_binary_path=args.jackhmmer_binary_path,
-                    hhblits_binary_path=args.hhblits_binary_path,
-                    hhsearch_binary_path=args.hhsearch_binary_path,
-                    uniref90_database_path=args.uniref90_database_path,
-                    mgnify_database_path=args.mgnify_database_path,
-                    bfd_database_path=args.bfd_database_path,
-                    uniclust30_database_path=args.uniclust30_database_path,
-                    pdb70_database_path=args.pdb70_database_path,
-                    use_small_bfd=use_small_bfd,
-                    no_cpus=args.cpus,
-                )
-                alignment_runner.run(fasta_path, local_alignment_dir)
-
-        feature_dict = data_processor.process_fasta(fasta_path=fasta_path,
-                                                    alignment_dir=local_alignment_dir)
-
+        # if global_is_multimer:
+        #     print("Multimer")
+        # else:
+        #     if (args.use_precomputed_alignments is None):
+        #         if not os.path.exists(local_alignment_dir):
+        #             os.makedirs(local_alignment_dir)
+        #         if args.enable_workflow:
+        #             print("Running alignment with ray workflow...")
+        #             alignment_data_workflow_runner = FastFoldDataWorkFlow(
+        #                 jackhmmer_binary_path=args.jackhmmer_binary_path,
+        #                 hhblits_binary_path=args.hhblits_binary_path,
+        #                 hhsearch_binary_path=args.hhsearch_binary_path,
+        #                 uniref90_database_path=args.uniref90_database_path,
+        #                 mgnify_database_path=args.mgnify_database_path,
+        #                 bfd_database_path=args.bfd_database_path,
+        #                 uniclust30_database_path=args.uniclust30_database_path,
+        #                 pdb70_database_path=args.pdb70_database_path,
+        #                 use_small_bfd=use_small_bfd,
+        #                 no_cpus=args.cpus,
+        #             )
+        #             t = time.perf_counter()
+        #             alignment_data_workflow_runner.run(fasta_path, output_dir=output_dir_base, alignment_dir=local_alignment_dir)
+        #             print(f"Alignment data workflow time: {time.perf_counter() - t}")
+        #         else:
+        #             alignment_runner = data_pipeline.AlignmentRunner(
+        #                 jackhmmer_binary_path=args.jackhmmer_binary_path,
+        #                 hhblits_binary_path=args.hhblits_binary_path,
+        #                 hhsearch_binary_path=args.hhsearch_binary_path,
+        #                 uniref90_database_path=args.uniref90_database_path,
+        #                 mgnify_database_path=args.mgnify_database_path,
+        #                 bfd_database_path=args.bfd_database_path,
+        #                 uniclust30_database_path=args.uniclust30_database_path,
+        #                 pdb70_database_path=args.pdb70_database_path,
+        #                 use_small_bfd=use_small_bfd,
+        #                 no_cpus=args.cpus,
+        #             )
+        #             alignment_runner.run(fasta_path, local_alignment_dir)
+
+        # feature_dict = data_processor.process_fasta(fasta_path=fasta_path,
+        #                                             alignment_dir=local_alignment_dir)
+
+        feature_dict = pickle.load(open("/home/lcmql/data/features_pdb1o5d.pkl", "rb"))
         # Remove temporary FASTA file
         os.remove(fasta_path)
 
@@ -289,6 +296,14 @@ if __name__ == "__main__":
                         default='full_dbs',
                         choices=('reduced_dbs', 'full_dbs'))
     parser.add_argument('--data_random_seed', type=str, default=None)
+    parser.add_argument(
+        "--model_preset",
+        type=str,
+        default="monomer",
+        choices=["monomer", "multimer"],
+        help="Choose preset model configuration - the monomer model, the monomer model with "
+        "extra ensembling, monomer model with pTM head, or multimer model",
+    )
     add_data_args(parser)
     args = parser.parse_args()